I'm sort of an "advanced beginner" when it comes to R, so this might seem like a trivial question. Suppose I'm using RsamTools to query through a Bam File. If I say I want everything between bp 3000000 and 3000500 in a certain chromosome I'll get results both on the negative and positive strand.
Suppose I get 3000010 on the negative strand with DNA string "CTCTTTTTT" ( the string is bigger but for the purpose of this questions I think it's ok ) . What does this mean from the following:
- Is that DNA string returned actually the positive strand complement of the matched sequence on the negative strand? or
- Is CTC the 5' end of the read on the negative strand? or
- Is CTC the 3'end of the read on the negative strand? or
- Did it actually match it from bp 3000010 on the negative strand? or
- Something else?